ENST00000648606.1:n.1621T>C

Variant names:

• chr6-163342620-A-G
• rs760887
• ENST00000648606.1:n.1621T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648606.1(ENSG00000285564):​n.1621T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 151,926 control chromosomes in the GnomAD database, including 13,942 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.42 (13942 hom., cov: 32)
• Consequence: ENSG00000285564 ENST00000648606.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184

Genes affected

ENSG00000285564 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DKFZp451B082	NR_033862.1	n.1884T>C		non_coding_transcript_exon_variant	Exon 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285564	ENST00000648606.1	n.1621T>C		non_coding_transcript_exon_variant	Exon 3 of 4
ENSG00000285564	ENST00000653903.1	n.1421T>C		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000285564	ENST00000659196.1	n.1433T>C		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63573 AN: 151806 Hom.: 13926 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.422

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.419 AC: 63623 AN: 151926 Hom.: 13942 Cov.: 32 AF XY: 0.418 AC XY: 31035 AN XY: 74226

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.464

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.478

Gnomad4 OTH AF: 0.424

Alfa AF: 0.442 Hom.: 1959

Bravo AF: 0.412

Asia WGS AF: 0.335 AC: 1163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.2
DANN	Benign	0.57

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs760887; hg19: chr6-163763652; COSMIC: COSV69432215;